Some of these have certainly already been posted before. I guess I am just backing them up.
Diplomacy option to cease war with a 3rd party. It sucks if you want to defend an ally, you have to also go to war with the nation they are hostile with. Shouldn't a powerful or rich 3rd party be able to bully or bribe a nation to cease war?
Cease fire and peace treaty should not be the same thing. As I recall in civ2 they were not. For one thing there would be different reputation reactions for breaking them. And sometimes you just want to fall back and recover a bit, get your people down from war weariness, and then resume the battle. You don't necessarily want to declare 20 turns of peace. And you know you can never trust the AI's peace treaties anyway.
I'm tired of polite civs attacking me out of nowhere. needs to be a better reputation / interciv relation scheme. For example one that tells me both how they feel about me, and whether they are hostile, as two separate pieces. Since they seem to be anyway.
I agree that multiple UU's would be nice. I dont know that they should all trigger GA's. But a civ will have multiple units with unique strengths that other civs will not. Like flavor units perhaps, but actually with different stats, instead of just different graphics. Then make the GA-triggering unit, even more powerful in comparison. That way each civ will have things (militarily) they are good at naturally, at different times.
Also perhaps different GA-triggering UU's for different ages, but have the ability to select, perhaps beforehand, which age you will get a GA.
Ability to name land features - couldn't this be done in SMAC? and also to share with allies the names of your land features for the purpose of common reference points. Especially in multiplayer - I don't care if the AI knows the name of a particular mountain range --- UNLESS one could make actual land agreements with the AI, like trading a "no build zone" for something, perhaps a different no build zone. (the value of this would be based on resources visible to each civ I suppose) I do this a fair amount in the type of multiplayer game I play, where I have a neighbor player and we agree on borders before our cities are even built. (not always though, since sometimes relations are forced to be strained from the beginning..)
The tech tree is also a bit silly. Who would learn the tech to work iron if they didn't have iron? Who would learn how to ride without horses? Perhaps alternate techs, for example if you didnt have metals, learn how to weave excellent armors from your native grasses or something. Of course your grass armor wouldn't be anywhere near as tough as your neighbor's swordsmen with plate steel. But it would be tougher than the cloth shirt you're stuck with otherwise.
Some things to be able to mod:
road system - some people like infinite movement railroads, others dont. I won't argue the point here (personally I like them). But it would be nice to have it moddable so those who don't like them, don't have to have them, etc. To be able to change the # of movement each type gives (with a checkbox for infinite I suppose), or even to be able to build more than just 2 types of roads. Also to have them "upgrade" from one age to another, again not necessarily vanilla, but moddable. Say in the ancient ages your roads give 2 movement, but then in the middle ages your roads are better, and they give 3. (or maybe at a particular tech advance IE engineering, or even stone road building)
frequency of golden ages - maybe someone wants to be able to trigger more than one GA per game.
number of tech ages in the game - not useful for regular stone age to present day and beyond civ, but for fantasy mods, or short time period mods, or mods with a lot more tech variety for whatever reason.
the ability to mod a completely different tech tree for each civ or at least culture group. So that one group can research certain things easily and not require, or maybe not even be able to research other things, which another group would research easily instead. different costs for different civs as well.
Again, I dont know if it would be useful for vanilla civ, but there are definitely mods that could use this.